Early epidemiological signatures of novel SARS-CoV-2 variants: establishment of B.1.617.2 in England

Abstract

The rapid emergence of SARS-CoV-2 mutants with new phenotypic properties is a critical challenge to the control of the ongoing pandemic. B.1.1.7 was monitored in the UK through routine testing and S-gene target failures (SGTF), comprising over 90% of cases by March 2021. Now, the reverse is occurring: SGTF cases are being replaced by an S-gene positive variant, which we associate with B.1.617.2. Evidence from the characteristics of S-gene positive cases demonstrates that, following importation, B.1.617.2 is transmitted locally, growing at a rate higher than B.1.1.7 and a doubling time between 5-14 days. S-gene positive cases should be prioritised for sequencing and aggressive control in any countries in which this variant is newly detected.One-Sentence SummaryThe B.1.617.2 variant of SARS-CoV-2 is replacing B.1.1.7 and emerging as the dominant variant in England, evidenced by sustained local transmission.

Herd immunity induced by COVID-19 vaccination programs and suppression of epidemics caused by the SARS-CoV-2 Delta variant in China

“…Efforts to increase population's confidence and willingness to be vaccinated will thus be of paramount importance to allow a return to a pre-COVID-19 lifestyle. Our study shows that the spread of new more transmissible (and possibly also more lethal [35][36][37][38][39][40][41][42] ) variants substantially increases herd immunity thresholds to level that may not be feasible in any population, so that mitigation strategies become much more relevant.…”

“…We consider a basic reproductive number (R0) of 2.5 according to estimates for the historical SARS-CoV-2 lineages in China [19][20][21]62 . Higher values (in the range 3.8-6) are used when other variants of concern are modeled [35][36][37][38][39][40][41][42] .…”

Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences

“…We also identified 22 patients with COVID-19 caused by B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants reported to be causing widespread disease and extensive public health problems in India, other Southeast Asian countries, and many regions of the UK (https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---8-june-2021, last accessed June 9, 2021). [43][44][45][46][47][48][49][50] These patients also had a high rate of hospitalization.…”

“…In the last half of May, depending on the specific day, the B.1.1.7 variant caused 63%-90% of J o u r n a l P r e -p r o o f new COVID-19 cases. In addition, we found that cases caused by variants P. [43][44][45][46][47][48][49][50] Variant B.1.617 is resistant to the monoclonal antibody Bamlanivimab (LY-Cov555), as assessed by an in vitro host-cell entry assay, 46 and B.1.617.1 has been reported to be highly virulent in hamsters following intranasal inoculation. 45 These two variants are characterized by a core group of amino acid replacements in spike protein: L452R, T478K or E484Q, D614G, and P681R (Figure 6).…”

“…J o u r n a l P r e -p r o o f understanding is needed of the factors underlying vaccine breakthrough infections, and studies are underway to examine potential contributors.Although extensive genomic data are not available, members of the B.1.617 variant family are contributing to the COVID-19 disease surge in India and other countries in Southeast Asia (https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---8june-2021, last accessed June 9, 2021) [43][44][45][46][47][48][49][50]. B.1.617 variants also have been documented to be increasing rapidly in many areas of the U.K., and have been estimated to be 60% more transmissible than B.1.1.7, the variant that rapidly rose to dominate new infections in the U.K 49,50,85. In this regard, the identification of 22 patients in the Houston metropolitan area infectedwith variants B.1.617.1 and B.1.617.2 is concerning.…”